empirical_incubation_dist: Extract empirical incubation period distribution from...

In epitrix: Small Helpers and Tricks for Epidemics Analysis

Extract empirical incubation period distribution from linelist data

Description

This function takes in a linelist data frame and extracts the empirical incubation period distribution and can take into account uncertainty in the dates of exposure.

Usage

empirical_incubation_dist(x, date_of_onset, exposure, exposure_end = NULL)

Arguments

x	the linelist data (data.frame or linelist object) containing at least a column containing the exposure dates and one containing the onset dates.
date_of_onset	the name of the column containing the onset dates (bare variable name or in quotes)
exposure	the name of the column containing the exposure dates (bare variable name or in quotes)
exposure_end	the name of a column containing dates representing the end of the exposure period. This is 'NULL' by default, indicating all exposures are known and in the 'exposure' column.

Value

a data frame containing a column with the different incubation periods and a column containing their relative frequency

Note

For exposure dates, each element can be a vector containing several possible exposure dates. Note that if the same exposure date appears twice in the list it is given twice as much weight.

Author(s)

Flavio Finger, [e-mail], Zhian N. Kamvar

Examples

if (require(tibble)) {
random_dates <- as.Date("2020-01-01") + sample(0:30, 50, replace = TRUE)
x <- tibble(date_of_onset = random_dates)

# Linelist with a list column of potential exposure dates ------------------
mkexposures <- function(x) x - round(rgamma(sample.int(5, size = 1), shape = 12, rate = 3))
exposures <- sapply(x$date_of_onset, mkexposures)
x$date_exposure <- exposures

incubation_period_dist <- empirical_incubation_dist(x, date_of_onset, date_exposure)
incubation_period_dist

# Linelist with exposure range ---------------------------------------------
start_exposure   <- round(rgamma(nrow(x), shape = 12, rate = 3))
end_exposure     <- round(rgamma(nrow(x), shape = 12, rate = 7))
x$exposure_end   <- x$date_of_onset - end_exposure
x$exposure_start <- x$exposure_end - start_exposure
incubation_period_dist <- empirical_incubation_dist(x, date_of_onset, exposure_start, exposure_end)
incubation_period_dist
plot(incubation_period_dist,
     type = "h", lwd = 10, lend = 2, col = "#49D193",
     xlab = "Days since exposure",
     ylab = "Probability",
     main = "Incubation time distribution")
}

epitrix documentation built on Aug. 8, 2025, 7:18 p.m.